Transcriptional Regulatory Networks in Saccharomyces cerevisiae

One of the main goals of systems biology is reverse engineering network structures from experimental data. Using quantitative networks measures, biological processes can be characterized and understood on a systems level. This paper reviews the scientific literature on the transcriptional regulatory networks of Saccharomyces cerevisiae to discuss what kind of structures can be identified and what this means biologically. This discussion comprises network characteristics, network dynamics in biological processes, and robustness; an inherent emergent property of networks.

[1]  Albert-László Barabási,et al.  Scale-Free Networks: A Decade and Beyond , 2009, Science.

[2]  Jianzhi Zhang,et al.  A Big World Inside Small-World Networks , 2009, PloS one.

[3]  Diogo M. Camacho,et al.  Systems Biology Strikes Gold , 2009, Cell.

[4]  D. Bernardo,et al.  A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches , 2009, Cell.

[5]  Hiroaki Kitano,et al.  Biological robustness , 2008, Nature Reviews Genetics.

[6]  Joshua E. S. Socolar,et al.  Global control of cell-cycle transcription by coupled CDK and network oscillators , 2008, Nature.

[7]  H. Kitano Towards a theory of biological robustness , 2007, Molecular systems biology.

[8]  J. Stark,et al.  Network motifs: structure does not determine function , 2006, BMC Genomics.

[9]  Rafael Sanjuán,et al.  Mechanisms of genetic robustness in RNA viruses , 2006, EMBO reports.

[10]  Andrzej Rucinski,et al.  Random graphs , 2006, SODA.

[11]  M. Elowitz,et al.  Reconstruction of genetic circuits , 2005, Nature.

[12]  Shuji Ishihara,et al.  Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes , 2005, Genes to cells : devoted to molecular & cellular mechanisms.

[13]  M. Gerstein,et al.  Genomic analysis of regulatory network dynamics reveals large topological changes , 2004, Nature.

[14]  S. Teichmann,et al.  Gene regulatory network growth by duplication , 2004, Nature Genetics.

[15]  A. Barabasi,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[16]  Jay D. Keasling,et al.  Metabolic engineering for drug discovery and development , 2003, Nature Reviews Drug Discovery.

[17]  O. Fiehn Faculty Opinions recommendation of Transcriptional regulatory networks in Saccharomyces cerevisiae. , 2002 .

[18]  David J. Galas,et al.  A duplication growth model of gene expression networks , 2002, Bioinform..

[19]  S. Shen-Orr,et al.  Network motifs: simple building blocks of complex networks. , 2002, Science.

[20]  A. Barabasi,et al.  Hierarchical Organization of Modularity in Metabolic Networks , 2002, Science.

[21]  S. Havlin,et al.  Scale-free networks are ultrasmall. , 2002, Physical review letters.

[22]  P. Bourgine,et al.  Topological and causal structure of the yeast transcriptional regulatory network , 2002, Nature Genetics.

[23]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[24]  J. Ferrell Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. , 2002, Current opinion in cell biology.

[25]  Martin Suter,et al.  Small World , 2002 .

[26]  H. Kitano Systems Biology: A Brief Overview , 2002, Science.

[27]  Lisa Chong,et al.  Whole-istic Biology , 2002, Science.

[28]  Andrey Rzhetsky,et al.  Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome , 2001, Bioinform..

[29]  Nicola J. Rinaldi,et al.  Serial Regulation of Transcriptional Regulators in the Yeast Cell Cycle , 2001, Cell.

[30]  Albert-László Barabási,et al.  Statistical mechanics of complex networks , 2001, ArXiv.

[31]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[32]  John Doyle,et al.  Complexity and robustness , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[33]  A. Barabasi,et al.  Error and attack tolerance of complex networks , 2000, Nature.

[34]  D. Fell,et al.  The small world inside large metabolic networks , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[35]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[36]  Ronald W. Davis,et al.  A genome-wide transcriptional analysis of the mitotic cell cycle. , 1998, Molecular cell.

[37]  Araceli M. Huerta,et al.  From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[38]  Marek S. Skrzypek,et al.  YPDTM, PombePDTM and WormPDTM: model organism volumes of the BioKnowledgeTM Library, an integrated resource for protein information , 2001, Nucleic Acids Res..

[39]  A. Barabasi,et al.  Emergence of Scaling in Random Networks , 1999 .

[40]  Xerox,et al.  The Small World , 1999 .

[41]  Sharon L. Milgram,et al.  The Small World Problem , 1967 .